Normally, when you change the view to Checked Out To Me on the Site Content and Structure page, you would see all checked out items throughout the site. Now, that view only works for the Farm Administrator account. Any other user can only see checked out files if they navigate to the specific library/folder in the library where the file resides. It worked in the past, but stopped about 3 months ago.
The users are members of a domain group that has full control permissions on the view. Also, the Files Checked Out to Me web part on the site default page works - they can see all of the files they have checked out in the site, but the actions that are available on the Site Content and Structure page are not available in that web part (like multiple check-in, etc).